Phylogenetic analyses confirm polyphyly of the genus Campanula (Campanulaceae s. str.), leading to a proposal for generic reappraisal

Previous phylogenetic analyses found that the largest genus in the tribe Campanuleae, Campanula L. is polyphyletic. The genus is extremely intermingled, involving more than 50 genera, but no generic reappraisal has been attempted. For undertaking further phylogenetic analyses and subsequent generic reappraisal of the tribe, we sampled 333 samples, representing 27 of 28 genera currently recognized. Among them, 146 samples and two genera, Cylindrocarpa Regel and Sergia Fed., were newly sequenced. Six chloroplast DNA loci (atpB-rbcL, matK, petD-intron, rbcL, rpl16, and trnL-F) and internal transcribed spacer were used to undertake phylogenetic analyses. Our chloroplast DNA phylogeny comprises 24 clades, that is, 18 Cam clades and six genera, Feeria Buser, Homocodon D. Y. Hong, Jasione L., Peracarpa Hook. f. & Thomson, Trachelium L., and Favratia Feer. Campanula species are scattered among the 18 Cam clades and the six genera, and some of them join with well-established genera like Phyteuma L. and Adenophora Fisch. In the phylogeny Musschia Dumort. is at the basal position, but Jasione's position is unclear, whether in the tribe Campanuleae or in Wahlenbergieae; the other 22 lineages are grouped into two major clades: clade A comprising Cam 13–17 plus Feeria and Trachelium, and clade B comprising Cam 02, 03, 04-1, 04-2, and 06-12 plus Homocodon and Peracarpa. We found that the molecular phylogeny is closely correlated with morphology, particularly pollen morphology: clade A with pollen 3-porate and capsule dehiscent mostly by basal pores; and clade B with pollen mostly 4 (5–15)-porate and capsule dehiscent mostly by apical-middle pores. A generic reappraisal of the tribe is suggested based on the integrated phylogenetic analyses.     

栓菌属和它的亲缘属属界划分的研究

栓菌属(Trametes) 自Fries(1835)建立迄今已有近150年的历史。Fries(1835),Patouillard(1900),Kotlaba & Pouzar(1957),的工作代表了对本属研究的三个比较重要的发展阶段。许多分类学家都认为栓菌属是多孔菌科(Polyporaceae,Basidiomycetes)中最混乱、最不易划清属间界限的一个类群。研究清楚这一属和它的亲缘属的属界以及它们之间的相互关系是研究多孔菌科分类中十分重要的课题。作者多年来在研究这一类群的过程中,常常遇到属界不清,它们之间的相互关系也不易搞清楚等问题。从文献中可以看出,有的种类似乎可以随便地从一个属转移到另一个属,正确与否不易确定。因此,感到搞清楚本属的属界是十分重要的。作者即是在这一情况下进行这一课题研究的。首先搞清楚栓菌属的发展历史,各分类学家对它的不同概念,最后提出作者对本属的概念。然后再搞清楚各亲缘属的属界与其相互关系。凡是作者承认的属都提出自己的概念。     

Phylogenetics of Lophodermium from pine

Lophodermium comprises ascomycetous fungi that are both needle-cast pathogens and asymptomatic endophytes on a diversity of plant hosts. It is distinguished from other genera in the family Rhytismataceae by its filiform ascospores and ascocarps that open by a longitudinal slit. Nucleotide sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA were used to infer phylogenetic relationships within Lophodermium. Twenty-nine sequences from approximately 11 species of Lophodermium were analyzed together with eight sequences from isolates thought to represent six other genera of Rhytismataceae: Elytroderma, Lirula, Meloderma, Terriera, Tryblidiopsis and Colpoma. Two putative Meloderma desmazieresii isolates occurred within the Lophodermium clade but separate from one another, one grouped with L. indianum and the other with L. nitens. An isolate of Elytroderma deformans also occurred within the Lophodermium clade but on a solitary branch. The occurrence of these genera within the Lophodermium clade might be due to problems in generic concepts in Rhytismataceae, such as emphasis on spore morphology to delimit genera, to difficulty of isolating Rhytismataceae needle pathogens from material that also is colonized by Lophodermium or to a combination of both factors. We also evaluated the congruence of host distribution and several morphological characters on the ITS phylogeny. Lophodermium species from pine hosts formed a monophyletic sister group to Lophodermium species from more distant hosts from the southern hemisphere, but not to L. piceae from Picea. The ITS topology indicated that Lophodermium does not show strict cospeciation with pines at deeper branches, although several closely related isolates have closely related hosts. Pathogenic species occupy derived positions in the pine clade, suggesting that pathogenicity has evolved from endophytism. A new combination is proposed, Terriera minor (Tehon) P.R. Johnst.     

Constituents of the fungi Daedalea quercina and Daedaleopsis confragosa var. tricolor

Phytochemical examination of solvent extracts of the wood-rotting fungi Daedalea quercina and Daedaleopsis confragosa var. tricolor led to the isolation of five new triterpene derivatives and some known fungal constituents. All structures were identified by one- and two-dimensional NMR spectroscopy and mass spectrometry. From Daedalea quercina, the new natural products 16-O-acetylpolyporenic acid C, 16alpha-acetoxy-24-methylene-3-oxolanost-8-en-21-oic acid, (+)-24-methylene-3,23-dioxolanost-8-en-26-oic acid, (+)-3beta,12beta-dihydroxy-24-methyl-23-oxolanost-8-en-26-oi c acid and 12beta,23-epoxy-3alpha,23-dihydroxy-24-methyllanost-8- en-26-oic acid could be isolated. From Daedaleopsis confragosa var. tricolor, the compounds 3alpha-carboxyacetoxyquercinic acid, 3alpha-carboxyacetoxy-24-methylene-23-oxolanost-8-en-2 6-oic acid and 5alpha,8alpha-epidioxyergosta-6,22-dien-3beta-ol were identified. These are the first described triterpene derivatives isolated from this fungus.     

基于ITS序列的栓菌属部分种的分子分类初步研究

栓菌属 Trametes 的一些近缘种宏观和微观形态学非常相近,传统分类学方法难于对其进行准确分类定位。测定了 34 个分类单元的 ITS(包括 5.8SrDNA)序列,并对得到的 43 个分类单元的 ITS 序列进行系统发生分析,构建了聚类分析树状图。该树状图显示,栓菌属类群与其他属类群明显分开,Trametes versicolor 聚类到一个高支持率的独立分支。形态学上定名为 T. hirsuta 和 T. pubescens 物种聚类到同一高支持率的独立分支,试验分析表明这两个种应视为同一物种。     

Phylogenetic comparison among the heterocystous cyanobacteria based on a polyphasic approach

Phylogenetic comparison has been done among the selected heterocystous cyanobacteria belonging to the sections IV and V. The hierarchical cluster analysis based on antibiotics sensitivity showed a distant relationship between the members of Nostocales and Stigonematales. Thus, multiple antibiotic resistance pattern used as marker provide easy, fast, and reliable method for strain discrimination and genetic variability. However, morphological, physiological (both based on principal component analysis) and biochemical analysis grouped true branching cyanobacteria along with the members of section IV. Molecular analysis based on 16S rRNA gene sequences revealed that Hapalosiphon welwitschii and Westiellopsis sp. were grouped in cluster I whereas Scytonema bohnerii, a false branching genera showed a close proximity with Calothrix brevissima in cluster II. Cluster III of clade 2 included Nostoc calcicola and Anabaena oryzae which proved the heterogeneity at the generic level. Cluster IV the largest group of clade 2 based on 16S rRNA gene sequences includes six strains of the genera Nostoc, Anabaena, and Cylindrospermum showing ambiguous evolutionary relationship. In cluster IV, Anabaena sp. and Anabaena doliolum were phylogenetically linked by sharing 99% sequence similarity. Probably, they were of the same genetic makeup but appear differently under the diverse physiological conditions. Section IV showed polyphyletic origin whereas section V showed monophyletic origin. Results suggested that either morphological or physiological or biochemical or molecular attribute is not sufficient to provide true diversity and phylogeny of the cyanobacteria at the generic level and thus, a polyphasic approach would be more appropriate and reliable.     

Molecular phylogeny of new world primates (Platyrrhini) based on beta2-microglobulin DNA sequences

Neotropical primates, traditionally grouped in the infraorder Platyrrhini, comprise 16 extant genera. Cladistic analyses based on morphological characteristics and molecular data resulted in topologic arrangements depicting disparate phylogenetic relationships, indicating that the evolution of gross morphological characteristics and molecular traits is not necessarily congruent. Here we present a phylogenetic arrangement for all neotropical primate genera obtained from DNA sequence analyses of the beta2-microglobulin gene. Parsimony, distance, and maximum likelihood analyses favored two families, Atelidae and Cebidae, each containing 8 genera. Atelids were resolved into atelines and pitheciines. The well-supported ateline clade branched into alouattine (Alouatta) and ateline (Ateles, Lagothrix, Brachyteles) clades. In turn, within the Ateline clade, Lagothrix and Brachyteles were well-supported sister groups. The pitheciines branched into well-supported callicebine (Callicebus) and pitheciine (Pithecia, Cacajao, Chiropotes) clades. In turn, within the pitheciine clade, Cacajao and Chiropotes were well-supported sister groups. The cebids branched into callitrichine (Saguinus, Leontopithecus, Callimico, Callithrix-Cebuella), cebine (Cebus, Saimiri), and aotine (Aotus) clades. While the callitrichine clade and the groupings of species and genera within this clade were all well supported, the cebine clade received only modest support, and the position of Aotus could not be clearly established. Cladistic analyses favored the proposition of 15 rather than 16 extant genera by including Cebuella pygmaea in the genus Callithrix as the sister group of the Callithrix argentata species group. These analyses also favored the sister grouping of Callimico with Callithrix and then of Leontopithecus with the Callithrix-Callimico clade.     

Phylogenetics of scutigeromorph centipedes (Myriapoda: Chilopoda) with implications for species delimitation and historical biogeography of the Australian and New Caledonian faunas

Phylogeny of the centipede order Scutigeromorpha has received recent attention from combined analyses of molecular and morphological data. Denser generic sampling, an additional marker (12S rRNA), and multiple specimens for selected species are used to explore phylogeny, biogeography and taxonomy of this charismatic group of centipedes. Among 55 specimens/27 species analysed for six genes are the first molecular data for the genera Dendrothereua , Pilbarascutigera , and Tachythereua , and previously unsampled species of Scutigerinae from Madagascar. Sampling density is especially increased for Thereuoneminae from Australia and New Caledonia. At the base of Scutigeromorpha, the split of Pselliodidae from Scutigerinidae + Scutigeridae is favoured by the optimal parameter set in combined analyses, but most suboptimal parameter sets instead unite pselliodids and scutigerinids. Dendrothereua is re-established for a Neotropical clade that variably resolves as sister to Tachythereua or separate from Scutigerinae, grouped with Pselliodidae and Scutigerinidae. As traditionally diagnosed, the genera that comprise most of Australian and New Caledonian diversity, Allothereua and Parascutigera , are mutually polyphyletic, though they unite as a well supported clade, sister to or including the Western Australian Pilbarascutigera . The main biogeographical signal within the Allothereua / Parascutigera clade is Western Australia as sister area to eastern Australia/New Caledonia, within which New Caledonian " Parascutigera " has a single origin under optimal parameter sets. Genetic variation within scutigeromorph species is appraised using samples of Scutigera coleoptrata throughout its native distribution plus presumed synanthropic records, and from the Allothereua/Parascutigera clade. Variation between six alleged narrow-range endemic species of Parascutigera in north Queensland is consistent with a single species.     

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.     

A preliminary phylogeny of the 'didymocarpoid Gesneriaceae' based on three molecular data sets: Incongruence with available tribal classifications

The 'didymocarpoid Gesneriaceae' (traditional subfam. Cyrtandroideae excluding Epithemateae) are the largest group of Old World Gesneriaceae, comprising 85 genera and 1800 species. We attempt to resolve their hitherto poorly understood generic relationships using three molecular markers on 145 species, of which 128 belong to didymocarpoid Gesneriaceae. Our analyses demonstrate that consistent topological relationships can be retrieved from data sets with missing data using subsamples and different combinations of gene sequences. We show that all available classifications in Old World Gesneriaceae are artificial and do not reflect natural relationships. At the base of the didymocarpoids are grades of clades comprising isolated genera and small groups from Asia and Europe. These are followed by a clade comprising the African and Madagascan genera. The remaining clades represent the advanced Asiatic and Malesian genera. They include a major group with mostly twisted capsules. The much larger group of remaining genera comprises exclusively genera with straight capsules and the huge genus Cyrtandra with indehiscent fruits. Several genera such as Briggsia, Henckelia, and Chirita are not monophyletic; Chirita is even distributed throughout five clades. This degree of incongruence between molecular phylogenies, traditional classifications, and generic delimitations indicates the problems with classifications based on, sometimes a single, morphological characters.     

Large-scale biogeographic patterns of vascular plant richness in North America: an analysis at the generic level

The richness pattern of native vascular plants in North America (north of Mexico) was studied at the generic level. North America was divided into thirteen geographical regions, which were latitudinally grouped into four horizontal zones (northern, north-middle, south-middle, and southern zones); and longitudinally grouped into three vertical zones (eastern, central, and western zones). The native vascular flora of North America consisted of 1904 genera in 235 families and eighty-three orders. Along the latitudinal gradient, generic richness (in terms of the number of genera) showed a striking increase with decreasing latitude. The southern zone had more than four times as many genera as did the northern zone (with a difference of 1436 genera). 93.3% of genera in the northern zone also occurred in the southern zone. Along the longitudinal gradient, the central zone had the highest generic richness and the eastern zone had the lowest, but the difference in generic richness between the two zones was only sixty-one genera. The western and eastern zones shared 60% or more of their genera. Generic richness of vascular plants in North America was highly correlated ( r =0.965) to available environmental energy (expressed by annual potential evapotranspiration).     

Phylogenetic systematics of the tribe Millettieae (Leguminosae) based on chloroplast trnK/matK sequences and its implications for evolutionary patterns in Papilionoideae

Phylogenetic relationships in the tribe Millettieae and allies in the subfamily Papilionoideae (Leguminosae) were reconstructed from chloroplast trnK/matK sequences. Sixty-two accessions representing 57 traditionally recognized genera of Papilionoideae were sampled, including 27 samples from Millettieae. Phylogenies were constructed using maximum parsimony and are well resolved and supported by high bootstrap values. A well-supported "core Millettieae" clade is recognized, comprising the four large genera Millettia, Lonchocarpus, Derris, and Tephrosia. Several other small genera of Millettieae are not in the core Millettieae clade. Platycyamus is grouped with Phaseoleae (in part). Ostryocarpus, Austrosteenisia, and Dalbergiella are neither in the core Millettieae or Phaseoleae clade. These taxa, along with core Millettieae and Phaseoleae, form a monophyletic sister group to Indigofereae. Cyclolobium and Poecilanthe are close to Brongniartieae. Callerya and Wisteria belong to a large clade that includes all the legumes that lack the inverted repeat in their chloroplast genome, which confirms previous rbcL and phytochrome gene family phylogenies. The evolutionary history of four characters was examined in Millettieae and allies: the presence of canavanine, inflorescence types, the dehiscence of pods, and the presence of winged pods. trnK/matK sequence analysis suggests that the presence of a pseudoraceme or pseudopanicle and the accumulation of nonprotein amino acids are phylogenetically informative for Millettieae and allies with only a few exceptions.     

TRADITIONAL GENERIC CONCEPTS VERSUS 18S rRNA GENE PHYLOGENY IN THE GREEN ALGAL FAMILY SELENASTRACEAE (CHLOROPHYCEAE, CHLOROPHYTA)

Coccoid green algae of the Selenastraceae were investigated by means of light microscopy, TEM, and 18S rRNA analyses to evaluate the generic concept in this family. Phylogenetic trees inferred from the 18S rRNA gene sequences showed that the studied species of autosporic Selenastraceae formed a well-resolved monophyletic clade within the DO group of Chlorophyceae. Several morphological characteristics that are traditionally used as generic features were investigated, especially the arrangement of autospores in the mother cells, colony formation, and pyrenoid structure. The parallel arrangement of autospores was confirmed for the genera Ankistrodesmus , Podohedriella , and Quadrigula. In mother cells of Monoraphidium and Kirchneriella , the autospores were arranged serially. Colony formation was either stable ( Quadrigula ) or variable ( Ankistrodesmus , Podohedriella ) within genera. All strains studied possessed naked or starch-covered pyrenoids within the chloroplast. The pyrenoid matrix was homogenous or penetrated by thylakoids. In contrast to considerations of traditional systematics, the present study showed that the presence and structure of pyrenoids are unsuitable for differentiation of genera in Selenastraceae. Furthermore, the molecular analyses showed that any morphological criterion considered so far is not significant for the systematics of the Selenastraceae on the generic level. Species assigned to different genera such as Ankistrodesmus and Monoraphidium were not monophyletic and therefore not distinguishable as separate genera. Species of Monoraphidium appeared in four different lineages of the Selenastraceae. Our phylogenetic analyses support earlier discussions to abandon the common practice of conceiving "small" genera (i.e. genera that are differentiated from other genera by only a few diacritic characteristics and that contain only a small number of species) and to reestablish "large" genera of Selenastraceae such as Ankistrodesmus.     

分子证据支持蓝药蓼和大铜钱叶蓼归入冰岛蓼属

蓝药蓼Polygonum cyanandrum Diels和大铜钱叶蓼P.forrestiiDiels是否应归于冰岛蓼属Koenigia至今未得到很好的解决。本文利用叶绿体DNA的atp B-rbc L序列来评价这两个物种的亲缘关系和属的归属。对这两个物种以及相关代表种的atp B-rbcL序列分析发现,该片段的长度有较大的变异。从753bp到902bp;存在丰富的系统发育变异位点。系统发育分析表明：蓝药蓼和大铜钱叶蓼与冰岛蓼丘islandica聚为支持率较高的分支。而蓼属Polygonum代表种和其他属的代表种组成另外的分支,表明这两个种应置于冰岛蓼属。这一结果与花粉和染色体证据相吻合。根据这些证据以及形态学特征,还对冰岛蓼属与蓼属的范围与界定进行了讨论。     

虎尾草亚科系统发育关系的初步研究

运用广义形态学性状对虎尾草亚科（Chloridoideae）进行系统发育分析。内类群包括虎尾草亚科52属的69种植物,代表虎尾草亚科的主要类群;芦竹亚科（Arundinoideae）扁芒草族（Danthonieae）的Centropodia和Danthonia被选作外类群。分支分析表明,虎尾草亚科是一个单系类群。其严格一致树包括A、B、C、D、E5个分支。两个大族画眉草族（Eragrostideae）和虎尾草族（Chlorideae）代表虎尾草亚科内部类群分化的两个方向,分开处理较合理。细穗草族（Leptureae）放到虎尾草族中较合理。冠芒草族（Pappophoreae）是虎尾草亚科的基部类群,与画眉草族近缘。我们的研究支持虎尾草亚科从旧世界向新世界扩散的地理分布假说,并提供了虎尾草亚科属上类群的系统发育关系的框架。     

Two new Kirschsteiniothelia species with Dendryphiopsis anamorphs cluster in Kirschsteiniotheliaceae fam. nov

Two new Kirschsteiniothelia species are proposed in this study; both were collected on decaying wood from Chiang Mai and Chiang Rai provinces in northern Thailand. The taxa were isolated and the morphological characters are described and illustrated. ITS, LSU and SSU combined sequence analysis showed taxa of Kirschsteiniothelia separating into three lineages: (i) K. elaterascus grouped within Morosphaeriaceae (Pleosporales); (ii) K. maritima clustered with Mytilinidion spp. as a sister group in the Mytilinidiaceae clade; and (iii) the two new Kirschsteiniothelia species, which produce Dendryphiopsis anamorphs in culture, clustered with K. aethiops (the generic type) and the anamorph D. atra. The new family Kirschsteiniotheliaceae is introduced to accommodate taxa grouping with K. aethiops. K. elaterascus is transferred to Morosphaeria (Morosphaeriaceae) and a new genus Halokirschteiniothelia is introduced to accommodate K. maritima (Mytilinidiaceae).     

Molecular phylogeny of the Australian frog genera Crinia, Geocrinia, and allied taxa (Anura: Myobatrachidae).

We present a mitochondrial gene tree for representative species of all the genera in the subfamily Myobatrachinae, with special emphasis on Crinia and Geocrinia. This group has been the subject of a number of long-standing taxonomic and phylogenetic debates. Our phylogeny is based on data from approximately 780 bp of 12S rRNA and 676 bp of ND2, and resolves a number of these problems. We confirm that the morphologically highly derived monotypic genera Metacrinia, Myobatrachus, and Arenophryne are closely related, and that Pseudophryne forms the sister group to these genera. Uperoleia and the recently described genus Spicospina are also part of this clade. Our data show that Assa and Geocrinia are reciprocally monophyletic and together they form a well-supported clade. Geocrinia is monophyletic and the phylogenetic relationships with the genus are fully resolved with two major species groups identified: G. leai, G. victoriana, and G. laevis; and G. rosea, G. alba, and G. vitellina (we were unable to sample G. lutea). We confirm that Taudactylus forms the sister group to the other myobatrachine genera, but our data are equivocal on the phylogenetic position of Paracrinia. The phylogenetic relationships among Crinia species are well resolved with strong support for a number of distinct monophyletic clades, but more data are required to resolve relationships among these major Crinia clades. Crinia tasmaniensis and Bryobatrachus nimbus form the sister clade to the rest of Crinia. Due to the lack of generic level synapomorphies for a Bryobatrachus that includes C. tasmaniensis, we synonymize Bryobatrachus with Crinia. Crinia georgiana does not form a clade distinct from other Crinia species and so our data do not support recognition of the genus Ranidella for other Crinia species. Crinia subinsignifera, C. pseudinsignifera, and C. insignifera are extremely closely related despite differences in male advertisement call. A preliminary investigation of phylogeographic substructure within C. signifera revealed significant divergence between samples from across the range of this species.     

Position of the genera Lycenchelys gill and Lycodapus gilbert in the family Zoarcidae (Perciformes: Zoarcoidei) inferred from molecular genetic analysis

Sequence variation ofthe mitochondrial COI, cytochrome b, and 16S RNA genes, as well as nuclear RNF213 gene was examined in the genera Lycenchelys and Lycodapus with the purpose of determination of their positions in the system of the family Zoarcidae. It was demonstrated that the genus Lycodapus was considerably closer to the generic group of Lycogramminae (Lycogrammoides, Bothrocara, Allolepis, Bothrocarhichthys) than the genus Lycenchelys. However, on the phylogenetic trees both of these genera were located in the clade of the subfamily Lycodinae. Genetic heterogeneity of the genus Lycenchelys, represented by two species groups differing in distribution patterns (northeastern Pacific and Antarctic) and showing more profound differences than the genera of subfamily Lycodinae, was demonstrated.